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Windows 7: Storage Device Issues, virus related?

Alright, I have started a thread in the Crashes and Debugging section, and it seems this issue has been pointed towards a virus that has not yet been properly gotten rid of.

A lot of the problems that it's caused are mentioned in this thread, so it would be a bit useful to read up on what has been attempted to fix this issue and what problems persist.

I've done some troubleshooting and attempts to determine the problem, being searching for drivers/services not starting properly within the registry and such.

If you have not checked out the thread linked above, some things I have taken note is:
- Removable Disk Drives are completely gone, missing from Disk Management and explorer, not to mention external storage devices do not appear in device manager. This will put USB drives in a non-responsive state to newly plugged in devices.

- Once USB drives are put in this "non-responsive" state, they will cause a BSOD upon shutting down. (BUGCODE_USB_DRIVER, 0xFE)

- It seems that cscript.exe (Which I have noticed is connected to several worms) seems to be running at all times, hiding from task manager. (Thanks for DDS for find that out.) I don't know if this is normal or not, however.

- Upon ending a random number of processes, Task Manager goes into a non-responding state, making the computer useless when it comes to opening/closing programs. This requires a hard shut off.

- A generic looking windows popup with a title of "You're about to be logged off." and saying "Windows will now shut down in less than a minute." appears whenever I ran a certain removal tool. It used to appear everyday at one random point, however a few virus scans in safe mode changed that.

I've got a few thing determined:
- My USB devices are working fine, the missing removable disk drives in Disk Management causes an issue when a device with any bit of storage is plugged in.

- This is not a "hardware issue." (as Microsoft's support tried suggesting...) External Drives show up in my BIOS.

- This problem has also appeared on my other hard drives. (Their Windows installations also have no removable disk drives.)

If anymore information is needed, let me know and I will obtain it for you. Any suggestions?

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